Seres Therapeutics, Inc.

Previous wording

Based on prior FDA feedback, we have continued preparations for a SER-155 Phase 2 study in allo-HSCT that could provide a time and capital-efficient path to obtaining clinical results. We require additional capital to begin this study. In May 2025, we filed the SER-155 Phase 2 protocol with the FDA and are awaiting feedback, which is expected to support finalizing the protocol. The SER-155 Phase 2 study is expected to enroll approximately 248 participants and incorporate an adaptive design and an interim data analysis when approximately half of the enrolled participants have reached the primary endpoint. We expect to obtain the interim clinical results within twelve months following study initiation, which we believe will facilitate timely engagement with the FDA on the design of a Phase 3 study and inform development in adjacent medically vulnerable patient populations. We believe that positive results, if achieved, from the Phase 2 study could enable advancement into a single Phase 3 trial to support registration.

Current wording

Based on prior FDA feedback, we are progressing start-up activities for our SER-155 Phase 2 study in allo-HSCT that could provide a time and capital-efficient path to obtaining clinical results. We require additional capital to begin this study. In May 2025, we filed the SER-155 Phase 2 protocol with the FDA. In September 2025, the FDA provided us with feedback on the SER-155 Phase 2 protocol and we continue to work with the FDA to finalize the study protocol. The SER-155 Phase 2 study will incorporate a well-powered, placebo-controlled design, which provides for a planned interim analysis to enable an expedited initial data readout. The SER-155 Phase 2 study is expected to enroll approximately 248 participants and incorporate an adaptive design and an interim data analysis when approximately half of the enrolled participants have reached the primary endpoint. We expect to obtain the interim clinical results within twelve months following study initiation, which we believe will facilitate timely engagement with the FDA on the design of a Phase 3 study and inform development in adjacent medically vulnerable patient populations. We believe that positive results, if achieved, from the Phase 2 study could enable advancement into a single Phase 3 trial to support registration.

Previous wording

Our product candidates are in early-stage clinical or preclinical development. Our ability to achieve profitability will depend heavily on the successful development and eventual commercialization of one or more of our product candidates. Since our inception, we have incurred significant operating losses. Our loss from operations was $52.1 million for the six months ended June 30, 2025. As of June 30, 2025, we had an accumulated deficit of $965.3 million.

Current wording

Our product candidates are in early-stage clinical or preclinical development. Our ability to achieve profitability will depend heavily on the successful development and eventual commercialization of one or more of our product candidates. Since our inception, we have incurred significant operating losses. Our loss from operations was $74.6 million for the nine months ended September 30, 2025. As of September 30, 2025, we had an accumulated deficit of $957.1 million.

Previous wording

As of June 30, 2025, we had cash and cash equivalents totaling $45.4 million. Based on our currently available cash resources, including the capital obtained from the Transaction, and considering our future operating plans and our ongoing obligations related to the Transaction, we anticipate that we will require additional funding in the first quarter of 2026. In accordance with applicable accounting standards, we evaluated whether there are conditions and events, considered in the aggregate, that raise substantial doubt about our ability to continue as a going concern within 12 months after the date of the issuance of the condensed consolidated financial statements included elsewhere in this Quarterly Report on Form 10-Q. In performing this analysis, we excluded certain elements of our operating plan that cannot be considered probable of occurring. Under the applicable accounting standards, any future transactions or equity issuances cannot be considered probable, as these events are outside our control. Accordingly, management has concluded that substantial doubt exists about our ability to continue as a going concern for 12 months from the date the condensed consolidated financial statements included elsewhere in this Quarterly Report on Form 10-Q, are issued. See “Risk Factors— Risks

Current wording

As of September 30, 2025, we had cash and cash equivalents totaling $47.6 million. Based on our currently available cash resources, including proceeds received in the fourth quarter from our at the market equity offering, and considering our future operating plans and our ongoing obligations related to the Transaction, we anticipate that we will fund our operations through the second quarter of 2026. In accordance with applicable accounting standards, we evaluated whether there are conditions and events, considered in the aggregate, that raise substantial doubt about our ability to continue as a going concern within 12 months after the date of the issuance of the condensed consolidated financial statements included elsewhere in this Quarterly Report on Form 10-Q. In performing this analysis, we excluded certain elements of our operating plan that cannot be considered probable of occurring. Under the applicable accounting standards, any future transactions or equity issuances cannot be considered probable, as these events are outside our control. Accordingly, management has concluded that substantial doubt exists about our ability to continue as a going concern for 12 months from the date the condensed consolidated financial statements included elsewhere in this Quarterly Report on Form 10-Q, are issued. See “Risk Factors— Risks Related to Our Financial Position and Need for Additional Capital —We have identified conditions and events that raise substantial doubt regarding our ability to continue as a going concern.”

Previous wording

As they are earned, the Milestone Payments will be satisfied as follows: (1) first, by set-off against all accrued interest on the Prepaid Milestone until the amount of such accrued interest has been paid in full, (2) second, by set-off against the outstanding balance of the Prepaid Milestone until the Prepaid Milestone has been repaid in full and (3) thereafter, in cash. If any amount of the Prepaid Milestone (and any accrued interest thereon) remains outstanding as of following the last day of the Milestone Period (defined below), the balance thereof (together with any interest accrued thereon) will be forgiven and the right of set-off of SPN with respect thereto will be deemed forfeited. The installment payment received on July 1, 2025 was offset by $1.4 million we paid to Nestlé on the same date related to certain employment obligations assumed by SPN with respect to the period ending as of the Closing Date.

Current wording

Prepaid Milestone (and any accrued interest thereon) remains outstanding as of following the last day of the Milestone Period (defined below), the balance thereof (together with any interest accrued thereon) will be forgiven and the right of set-off of SPN with respect thereto will be deemed forfeited. The installment payment received on July 1, 2025 was offset by $1.4 million we paid to Nestlé on the same date related to certain employment obligations assumed by SPN with respect to the period ending as of the Closing Date.

Previous wording

We estimated the costs associated with these future payments and recorded them within accrued liabilities due to SPN - related party on our condensed consolidated balance sheets as of the Closing. The contingent liabilities are remeasured at each reporting period based on (i) cash payments made by the Company to reduce the accrued liabilities due to SPN - related party and (ii) revised estimates of the total remaining liabilities due to SPN - related party. As of June 30, 2025, the contingent liabilities included $8.0 million associated with the Profit Sharing Payments, $2.8 million associated with the MSK Agreement, $0.9 million associated with our obligation to pay 80.1% of the costs associated with the lease of the Waltham facility through December 31, 2025, $1.4 million associated with certain employment-related costs for conveying employees, and $0.4 million associated with our ongoing post-marketing safety study of VOWST. We recorded a gain of $0.2 million for the three months ended June 30, 2025 primarily as a result of actual post-marketing safety study costs that were lower than the previous estimate.

Current wording

We estimated the costs associated with these future payments and recorded them within accrued liabilities due to SPN - related party on our condensed consolidated balance sheets as of the Closing. The contingent liabilities are remeasured at each reporting period based on (i) cash payments made by the Company to reduce the accrued liabilities due to SPN - related party and (ii) revised estimates of the total remaining liabilities due to SPN - related party. As of September 30, 2025, the contingent liabilities included $1.7 million associated with the Profit Sharing Payments, $2.2 million associated with the MSK Agreement, $0.4 million associated with our obligation to pay 80.1% of the costs associated with the lease of the Waltham facility through December 31, 2025, and $0.2 million associated with the ongoing post-marketing safety study of VOWST. We recorded a gain of $2.2 million for the three months ended September 30, 2025 primarily as a result of SPN's actual and forecasted Profit Sharing Payments as compared to the previous estimate.

Previous wording

In connection with the Closing, we entered into a cross-license agreement with SPN under which, we granted to SPN a perpetual, worldwide, non-exclusive, fully paid-up license under certain Seres patents that have been issued or will issue in the future and current know-how controlled by us that is not transferred to SPN pursuant to the Purchase Agreement. In the field of the treatment of Clostridioides difficile infections, or CDI, and rCDI and associated complications, or collectively, the CDI Field, the license to SPN under such Seres patents and know-how is exclusive to SPN for five years after the Closing and co-exclusive between SPN and Seres following that five year period. The license from Seres to SPN is to issued Seres patents that currently or in the future cover the

Current wording

In connection with the Closing, we entered into a cross-license agreement with SPN under which, we granted to SPN a perpetual, worldwide, non-exclusive, fully paid-up license under certain Seres patents that have been issued or will issue in the future and current know-how controlled by us that is not transferred to SPN pursuant to the Purchase Agreement. In the field of the treatment of Clostridioides difficile infections, or CDI, and rCDI and associated complications, or collectively, the CDI Field, the license to SPN under such Seres patents and know-how is exclusive to SPN for five years after the Closing and co-exclusive between SPN and Seres following that five year period. The license from Seres to SPN is to issued Seres patents that currently or in the future cover the Product or improvements thereof and know-how that is used or reasonably useful in connection with the exploitation of the VOWST Business. See “Intellectual Property” below.

Previous wording

Based on prior FDA feedback, we have continued preparations for a SER-155 Phase 2 study in allo-HSCT that could provide a time and capital-efficient path to obtaining clinical results. We require additional capital to begin this study. In May 2025, we filed the SER-155 Phase 2 protocol with the FDA and are awaiting feedback, which is expected to support finalizing the protocol. The SER-155 Phase 2 study is expected to enroll approximately 248 participants and incorporate an adaptive design and an interim data analysis when approximately half of the enrolled participants have reached the primary endpoint. We expect to obtain the interim clinical results within twelve months following study initiation, which we believe will facilitate timely engagement with the FDA on the design of a Phase 3 study and inform development in adjacent medically vulnerable patient populations. We believe that positive results, if achieved, from the Phase 2 study could enable advancement into a single Phase 3 trial to support registration.

Current wording

Based on prior FDA feedback, we are progressing start-up activities for our SER-155 Phase 2 study in allo-HSCT that could provide a time and capital-efficient path to obtaining clinical results. We require additional capital to begin this study. In May 2025, we filed the SER-155 Phase 2 protocol with the FDA. In September 2025, the FDA provided us with feedback on the SER-155 Phase 2 protocol and we continue to work with the FDA to finalize the study protocol. The SER-155 Phase 2 study will incorporate a well-powered, placebo-controlled design, which provides for a planned interim analysis to enable an expedited initial data readout. The SER-155 Phase 2 study is expected to enroll approximately 248 participants and incorporate an adaptive design and an interim data analysis when approximately half of the enrolled participants have reached the primary endpoint. We expect to obtain the interim clinical results within twelve months following study initiation, which we believe will facilitate timely engagement with the FDA on the design of a Phase 3 study and inform development in adjacent medically vulnerable patient populations. We believe that positive results, if achieved, from the Phase 2 study could enable advancement into a single Phase 3 trial to support registration.

Previous wording

We have an extensive patent portfolio directed to rationally designed ecologies of spores and microbes. The portfolio includes both company-owned patents and applications, and those that we have rights to as licensee. The patents and applications included in our portfolio cover both composition of matter and methods (e.g., method of treating). Our intellectual property rights related to SER-155 and SER-147 extend through at least 2043 (not including any potential term extension). We plan on continuing to broaden our patent portfolio. Currently, we have 23 active patent families, which includes 20 nationalized applications and three at the provisional stage. To date, we have obtained issuance of 32 U.S. patents (which includes three as licensee). Of the issued U.S. patents, 13 U.S. patents (including one as licensee) have been assigned to Nestlé Health Science as part of its purchase of VOWST.

Current wording

We have an extensive patent portfolio directed to rationally designed ecologies of spores and microbes. The portfolio includes both company-owned patents and applications, and those that we have rights to as licensee. The patents and applications included in our portfolio cover both composition of matter and methods (e.g., method of treating). Our intellectual property rights related to SER-155 and SER-147 extend through at least 2043 (not including any potential term extension). We plan on continuing to broaden our patent portfolio. Currently, we have 24 active patent families, which includes 20 nationalized applications and four at the provisional stage. To date, we have obtained issuance of 33 U.S. patents (which includes three as licensee). Of the issued U.S. patents, 13 U.S. patents (including one as licensee) have been assigned to Nestlé Health Science as part of its purchase of VOWST.

Previous wording

expenses incurred under agreements with third parties, including contract research organizations, or CROs, that conduct research, preclinical activities and clinical trials on our behalf as well as contract manufacturing organizations that manufacture drug products for use in our preclinical and clinical trials;

Current wording

expenses incurred under agreements with third parties, including contract research organizations, or CROs, that conduct research, preclinical activities and clinical trials on our behalf as well as contract manufacturing organizations and other third parties that manufacture or test drug products for use in our preclinical and clinical trials;

Previous wording

Research and development activities are central to our business model. Product candidates in later stages of clinical development generally have higher development costs than those in earlier stages of clinical development, primarily due to the increased size and duration of later-stage clinical trials. We anticipate an overall decrease in research and development expenses in 2025 as compared to 2024, following the sale of VOWST Business, completion of the Phase 1b study of SER-155 in allo-HSCT, development activities other than the completion of the SER-155 Phase 1b study, and costs associated with preparing for the next study of SER-155 in allo-HSCT. Research and development expenses may increase in the future if and as we resume development of any clinical or preclinical programs. In 2025, research and development expenses continue to include labor and passthrough costs, reimbursable by Nestlé, incurred in performing obligations under the TSA.

Current wording

Research and development activities are central to our business model. Product candidates in later stages of clinical development generally have higher development costs than those in earlier stages of clinical development, primarily due to the increased size and duration of later-stage clinical trials. We anticipate an overall decrease in research and development expenses in 2025 as compared to 2024, following the sale of the VOWST Business and completion of the Phase 1b study of SER-155 in allo-HSCT. Research and development expenses may increase in the future if and as we continue the clinical development of SER-155 in patients undergoing allo-HSCT and for other medically vulnerable populations and resume development of any other clinical or preclinical programs. In 2025, research and development expenses continue to include labor and passthrough costs, reimbursable by Nestlé, incurred in performing obligations under the TSA.

Previous wording

Since our inception in 2010, we have not recorded any U.S. federal or state income tax benefits for the net losses we have incurred in each year or our earned research and development tax credits, due to our uncertainty of realizing a benefit from those items. We did not provide for any income taxes in the three and six months ended June 30, 2025 or 2024.

Current wording

Since our inception in 2010, we have not recorded any U.S. federal or state income tax benefits for the net losses we have incurred in each year or our earned research and development tax credits, due to our uncertainty of realizing a benefit from those items. We did not provide for any income taxes in the three and nine months ended September 30, 2025 or 2024.

Previous wording

Our condensed consolidated financial statements are prepared in accordance with accounting principles generally accepted in the United States. The preparation of these condensed consolidated financial statements requires the application of appropriate technical accounting rules and guidance, as well as the use of estimates. The application of these policies necessarily involves judgments regarding future events. These estimates and judgments, in and of themselves, could materially impact the condensed consolidated financial statements and disclosures based on varying assumptions. The accounting policies discussed in our Annual Report on Form 10-K for the fiscal year ended December 31, 2024, filed with the SEC on March 13, 2025, or the Annual Report, are considered by management to be the most important to an understanding of the consolidated financial statements because of their significance to the portrayal of our financial condition and results of operations. There have been no material changes to that information disclosed in our Annual Report during the three and six months ended June 30, 2025.

Current wording

Our condensed consolidated financial statements are prepared in accordance with accounting principles generally accepted in the United States. The preparation of these condensed consolidated financial statements requires the application of appropriate technical accounting rules and guidance, as well as the use of estimates. The application of these policies necessarily involves judgments regarding future events. These estimates and judgments, in and of themselves, could materially impact the condensed consolidated financial statements and disclosures based on varying assumptions. The accounting policies discussed in our Annual Report on Form 10-K for the fiscal year ended December 31, 2024, filed with the SEC on March 13, 2025, or the Annual Report, are considered by management to be the most important to an understanding of the consolidated financial statements because of their significance to the portrayal of our financial condition and results of operations. There have been no material changes to that information disclosed in our Annual Report during the three and nine months ended September 30, 2025.

Previous wording

a decrease in personnel-related costs of $0.8 million primarily due to a decrease in salaries, bonus, employee benefits expenses, and stock-based compensation expense due to lower headcount;

Current wording

a decrease in personnel-related costs of $2.1 million primarily due to a decrease in salaries, bonuses, employee benefits expenses, and stock-based compensation expense due to lower headcount;

Previous wording

a decrease of $0.9 million in expenses related to our live biotherapeutics platform and research and development operations due to a decrease of $0.4 million of facilities and depreciation expense, as well as decreases of $0.3 million of employee-related costs, and decreases in other costs including lab assays and clinical storage costs, and

Current wording

a decrease of $1.3 million in expenses related to our live biotherapeutics platform and research and development operations due to a decrease of $0.5 million of facilities and depreciation expense, $0.5 million of lab assays and clinical storage costs, as well as $0.3 million of consulting and other costs, and

Previous wording

a decrease of $1.2 million in expenses related to our SER-155 program due to lower clinical trial costs as the Phase 1b study has largely been completed.

Current wording

a decrease of $0.4 million in expenses related to our SER-155 program due to lower clinical trial costs of $0.7 million as the Phase 1b study has largely been completed, partially offset by an increase of $0.2 million of lab supplies and consumables due to the commencement of manufacturing for the planned Phase 2 study.

Previous wording

General and administrative expenses were $10.3 million for the three months ended June 30, 2025 compared to $13.1 million for the three months ended June 30, 2024. The decrease of $2.8 million was primarily due to the following:

Current wording

General and administrative expenses were $9.5 million for the three months ended September 30, 2025 compared to $12.7 million for the three months ended September 30, 2024. The decrease of $3.2 million was primarily due to the following:

Previous wording

a decrease in personnel-related costs of $2.0 million primarily due to a decrease in salaries, bonus, employee benefits expenses, and stock-based compensation expenses due to the decrease in headcount period over period; and

Current wording

a decrease in personnel-related costs of $1.7 million primarily due to a decrease in salaries, bonuses, employee benefits expenses, and stock-based compensation expenses due to lower headcount; and

Previous wording

a decrease in facility-related and other costs of $0.9 million primarily related to headcount-based information technology costs that were reduced following the decrease in headcount.

Current wording

a decrease in facility-related and other costs of $1.3 million primarily related to headcount-based information technology costs that were reduced as a result of lower headcount.

Previous wording

Manufacturing services costs began with the effectiveness of the TSA with Nestlé in the fourth quarter of 2024 and resulted in $1.7 million of expenses for the three months ended June 30, 2025. The expenses are associated with the PRMS manufacturing performed on behalf of Nestlé, including labor, materials, allocated facility-related, lab supplies and other manufacturing costs that would have been capitalized into inventory prior to the sale of VOWST Business.

Current wording

Manufacturing services costs began with the effectiveness of the TSA with Nestlé in the fourth quarter of 2024 and resulted in $0.7 million of expenses for the three months ended September 30, 2025. The expenses are associated with the PRMS manufacturing performed on behalf of Nestlé, including labor, materials, allocated facility-related, lab supplies and other manufacturing costs that would have been capitalized into inventory prior to the sale of VOWST Business.

Previous wording

The following table summarizes our results of operations for the six months ended June 30, 2025 and 2024:

Current wording

The following table summarizes our results of operations for the nine months ended September 30, 2025 and 2024:

Previous wording

a decrease of $4.9 million in expenses related to our live biotherapeutics platform and research and development operations due to a decrease of $3.9 million of facilities and depreciation expense primarily related to the impairment charge that we recorded in the first quarter of 2024, as well as decreases of $0.5 million of employee-related costs, $0.3 million of clinical storage costs, and $0.2 million of lab assays, and

Current wording

a decrease of $6.2 million in expenses related to our live biotherapeutics platform and research and development operations due to a decrease of $4.4 million of facilities and depreciation expense primarily related to the impairment charge that we recorded in the first quarter of 2024, as well as decreases of $0.7 million of consulting and other costs, $0.5 million of clinical storage costs, and $0.5 million of lab assays;

Previous wording

a decrease in personnel-related costs of $2.5 million primarily due to a decrease in salaries, bonus, employee benefits expenses, and stock-based compensation expense due to lower headcount;

Current wording

a decrease in personnel-related costs of $4.7 million primarily due to a decrease in salaries, bonuses, employee benefits expenses, and stock-based compensation expense due to lower headcount, and

Previous wording

General and administrative expenses were $22.1 million for the six months ended June 30, 2025 compared to $28.0 million for the six months ended June 30, 2024. The decrease of $5.9 million was primarily due to the following:

Current wording

General and administrative expenses were $31.6 million for the nine months ended September 30, 2025 compared to $40.7 million for the nine months ended September 30, 2024. The decrease of $9.1 million was primarily due to the following:

Previous wording

a decrease in personnel-related costs of $4.4 million primarily due to a decrease in salaries, bonus, employee benefits expenses, and stock-based compensation expenses due to the decrease in headcount period over period; and

Current wording

a decrease in personnel-related costs of $6.2 million primarily due to a decrease in salaries, bonuses, employee benefits expenses, and stock-based compensation expenses due to lower headcount; and

Previous wording

a decrease in facility-related and other costs of $2.0 million primarily related to headcount-based information technology costs that were reduced following the decrease in headcount, as well as impairment charges recorded in the first quarter of 2024 related to our idled donor collection facility in Cambridge, Massachusetts.

Current wording

a decrease in facility-related and other costs of $3.3 million primarily related to headcount-based information technology costs that were reduced as a result of lower headcount, as well as impairment charges recorded in the first quarter of 2024 related to our idled donor collection facility in Cambridge, Massachusetts.

Previous wording

These decreases were partially offset by an increase in professional fees of $0.6 million due to an increase in consulting fees, which were primarily related to information technology consultants engaged to assist with the TSA, which costs are reimbursable by Nestlé.

Current wording

These decreases were partially offset by an increase in professional fees of $0.4 million due to an increase in legal and consulting fees.

Previous wording

Manufacturing services costs began with the effectiveness of the TSA with Nestlé in the fourth quarter of 2024 and resulted in $5.2 million of expenses for the six months ended June 30, 2025. The expenses are associated with the PRMS manufacturing performed on behalf of Nestlé, including labor, materials, allocated facility-related, lab supplies and other manufacturing costs that would have been capitalized into inventory prior to the sale of VOWST Business.

Current wording

Manufacturing services costs began with the effectiveness of the TSA with Nestlé in the fourth quarter of 2024 and resulted in $6.0 million of expenses for the nine months ended September 30, 2025. The expenses are associated with the PRMS manufacturing performed on behalf of Nestlé, including labor, materials, allocated facility-related, lab supplies and other manufacturing costs that would have been capitalized into inventory prior to the sale of VOWST Business.

Previous wording

Other income, net was $64.9 million and $4.2 million for the six months ended June 30, 2025 and 2024, respectively. The $60.7 million increase in other income, net was primarily due to the $50.0 million installment payment received from Nestlé in January 2025 that was conditioned on the Company’s material compliance with obligations under the TSA, $9.8 million of reimbursement income from Nestlé associated with the performance of TSA services, as well as a $2.4 million gain as a result of a change in estimate of the accrued liabilities due to SPN - related party. The increases were partially offset by a decrease in interest income of $1.7 million due to our lower cash balance.

Current wording

Other income (expense), net was $95.6 million of income and $17.7 million of expense for the nine months ended September 30, 2025 and 2024, respectively. The $113.3 million increase in other income, net was primarily due to the $50.0 million and $25.0 million installment payments received from Nestlé in January 2025 and July 2025, respectively, which were conditioned on our material compliance with obligations under the TSA, $11.8 million of reimbursement income from Nestlé associated with the performance of TSA services, as well as a $4.6 million gain as a result of a change in estimate of the accrued liabilities due to SPN - related party, and $0.6 million increase in sublease income. The increases were partially offset by a decrease in interest income of $1.7 million due to our lower cash balance. Additionally, the nine months ended September 30, 2024 included a $23.4 million loss associated with the extinguishment of the Oaktree Term Loan recorded inconnection with the sale of the VOWST Business to SPN.

Previous wording

Since our inception, we have generated revenue only from collaborations and have incurred recurring net losses. We anticipate that we will continue to incur losses for at least the next several years. We will need additional capital to fund our operations, which include our research and development and general and administrative expenses, which we may obtain from additional financings, public offerings, research funding, additional collaborations, contract and grant revenue or other sources.

Current wording

Since our inception, we have generated revenue only from collaborations and have incurred recurring losses from operations. We anticipate that we will continue to incur losses for at least the next several years. We will need additional capital to fund our operations, which include our research and development and general and administrative expenses, which we may obtain from additional financings, public offerings, research funding, additional collaborations, contract and grant revenue or other sources.

Previous wording

In May 2021, we entered into a Sales Agreement, or the Sales Agreement, with Cowen and Company, LLC, or Cowen, to sell shares of our common stock, with aggregate gross sales proceeds of up to $150.0 million, from time to time, through an “at the market” equity offering program under which Cowen acts as sales agent. As of June 30, 2025, we have sold 1,503,956 shares of common stock under the Sales Agreement, at an average price of approximately $32.65 per share, raising aggregate net proceeds of approximately $47.1 million after deducting an aggregate commission of approximately 3% and other issuance costs.

Current wording

In May 2021, we entered into a Sales Agreement, or the Sales Agreement, with Cowen and Company, LLC, or Cowen, to sell shares of our common stock, with aggregate gross sales proceeds of up to $150.0 million, from time to time, through an “at the market” equity offering program under which Cowen acts as sales agent. As of October 31, 2025, we have sold 1,772,037 shares of common stock under the Sales Agreement, at an average price of approximately $30.66 per share, raising aggregate net proceeds of approximately $52.2 million after deducting an aggregate commission of approximately 3% and other issuance costs.

Previous wording

As of June 30, 2025, we had cash and cash equivalents totaling $45.4 million and an accumulated deficit of $965.3 million. For the six months ended June 30, 2025, we incurred a loss from continuing operations of $52.1 million. We expect that our operating losses and negative cash flows will continue for the foreseeable future.

Current wording

As of September 30, 2025, we had cash and cash equivalents totaling $47.6 million and an accumulated deficit of $957.1 million. For the nine months ended September 30, 2025, we incurred a loss from operations of $74.6 million. We expect that our operating losses and negative cash flows will continue for the foreseeable future.

Previous wording

Under applicable accounting standards, we have the responsibility to evaluate whether conditions or events raise substantial doubt about our ability to meet our future financial obligations as they become due within 12 months after the date the consolidated financial statements are issued. The ability to obtain sufficient proceeds from additional equity offerings, collaborations or other financing with terms favorable or acceptable to us cannot be considered probable, as these events are outside of our control. Based on our currently available cash resources, including the capital obtained from the Transaction, and considering our future operating plans and our ongoing obligations related to the Transaction, we anticipate that we will require additional funding in the first quarter of 2026. Accordingly, management has concluded that these circumstances raise substantial doubt about our ability to continue as a going concern. Substantial doubt about our ability to continue as a going concern may materially and adversely affect the price per share of our common stock, and it may be more difficult for us to obtain financing. If potential collaborators decline to do business with us or potential investors decline to participate in any future financings due to such concerns, our ability to increase our cash position may be limited. We will need to generate significant revenues to achieve profitability, and we may never do so. Because of the numerous risks and uncertainties associated with the development of our current and any future product candidates, the development of our platform and technology and because the extent to which we may enter into collaborations with third parties for development of any of our product candidates is unknown, we are unable to estimate the amounts of increased capital outlays and operating expenses required for completing the research and development of our product candidates.

Current wording

Under applicable accounting standards, we have the responsibility to evaluate whether conditions or events raise substantial doubt about our ability to meet our future financial obligations as they become due within 12 months after the date the consolidated financial statements are issued. The ability to obtain sufficient proceeds from additional equity offerings, collaborations or other financing with terms favorable or acceptable to us cannot be considered probable, as these events are outside of our control. Based on our currently available cash resources, including proceeds received in the fourth quarter from our at the market equity offering, and considering our future operating plans and our ongoing obligations related to the Transaction, we anticipate that we will fund our operations through the second quarter of 2026. Accordingly, management has concluded that these circumstances raise substantial doubt about our ability to continue as a going concern. Substantial doubt about our ability to continue as a going concern may materially and adversely affect the price per share of our common stock, and it may be more difficult for us to obtain financing. If potential collaborators decline to do business with us or potential investors decline to participate in any future financings due to such concerns, our ability to increase our cash position may be limited. We will need to generate significant revenues to achieve profitability, and we may never do so. Because of the numerous risks and uncertainties associated with the development of our current and any future product candidates, the development of our platform and technology and because the extent to which we may enter into collaborations with third parties for development of any of our product candidates is unknown, we are unable to estimate the amounts of increased capital outlays and operating expenses required for completing the research and development of our product candidates.

Previous wording

During the six months ended June 30, 2025, cash provided by operating activities was $13.6 million due to net income of $12.8 million and non-cash charges of $11.4 million, partially offset by changes in our operating assets and liabilities of $10.6 million. Non-cash charges consisted of stock-based compensation expense of $5.2 million, $4.1 million related to the amortization of right-of-use assets, and $2.1 million of depreciation and amortization. Changes in our operating assets and liabilities during the six months ended June 30, 2025 consisted of a decrease in accrued liabilities due to SPN of $4.3 million, a decrease in operating lease liabilities of $4.2 million, a decrease in accrued expenses and other current and long-term liabilities of $4.8 million, and a decrease in accounts payable of $1.9 million, partially offset by a decrease in prepaid expenses and other current and other non-current assets of $3.4 million and a decrease in accounts receivable due from SPN of $1.2 million.

Current wording

During the nine months ended September 30, 2025, cash provided by operating activities was $15.8 million due to net income of $21.0 million and non-cash charges of $17.1 million, partially offset by changes in our operating assets and liabilities of $22.3 million. Non-cash charges consisted of stock-based compensation expense of $7.6 million, $6.2 million related to the amortization of right-of-use assets, and $3.2 million of depreciation and amortization. Changes in our operating assets and liabilities during the nine months ended September 30, 2025 consisted of a decrease in accrued liabilities due to SPN of $13.3 million, a decrease in operating lease liabilities of $6.4 million, a decrease in accrued expenses and other current and long-term liabilities of $4.2 million, a decrease in accounts payable of $2.4 million, and an increase in accounts receivable relating to the CARB-X program of $0.4 million, partially offset by a decrease in prepaid expenses and other current and other non-current assets of $2.7 million, and a decrease in accounts receivable due from SPN of $1.6 million.

Previous wording

During the six months ended June 30, 2024, operating activities used $75.0 million of cash, primarily due to a net loss of $73.0 million and changes in our operating assets and liabilities of $25.8 million, partially offset by non-cash charges of $23.7 million. Non-cash charges consisted of stock-based compensation expense of $12.0 million, $4.8 million related to the amortization of right-of-use assets, $3.0 million of depreciation and amortization, $1.0 million of amortization of debt issuance costs, $0.3 million loss on disposal of fixed assets, and $3.3 million of impairment charges related to our long-lived assets. These were partially offset by a $0.5 million decrease in the fair value of warrants. Changes in our operating assets and liabilities during the six months ended June 30, 2024 consisted of a decrease in operating lease liabilities of $2.3 million, an increase in inventories of $23.4 million related to the capitalization of VOWST manufacturing costs during the period, and an increase in collaboration receivable - related party of $9.9 million, partially offset by an increase in accrued expenses and other current and long-term liabilities of $5.8 million, a decrease in prepaid expenses and other current and other noncurrent assets of $2.5 million, an increase in deferred income - related party of $0.2 million, and an increase in accounts payable of $1.2 million.

Current wording

During the nine months ended September 30, 2024, operating activities used $109.7 million of cash, primarily due to non-cash charges of $90.1 million and changes in our operating assets and liabilities of $35.4 million, partially offset by net income of $15.8 million. Non-cash charges consisted of stock-based compensation expense of $17.2 million, $7.2 million related to the amortization of right-of-use assets, $4.4 million of depreciation and amortization, $1.4 million of amortization of debt issuance costs, $23.4 million of loss associated with the extinguishment of the Oaktree Term Loan, $0.3 million loss on disposal of fixed assets, and $3.3 million of impairment charges related to our long-lived assets. These were partially offset by the $146.7 million gain on sale of VOWST Business and $0.5 million decrease in the fair value of warrants. Changes in our operating assets and liabilities during the nine months ended September 30, 2024 consisted of a decrease in operating lease liabilities of $4.4 million, a decrease in deferred income - related party of $4.1 million, a decrease in accrued expenses and other current and long-term liabilities of $3.3 million, and a decrease in inventories of $33.8 millionin connection with the sale of the VOWST Business to SPN, partially offset by a decrease in collaboration receivable - related party of $8.7 million, a decrease in prepaid expenses and other current and other non-current assets of $0.3 million, and an increase in accounts payable of $1.2 million.

Previous wording

During the six months ended June 30, 2025, net cash used in investing activities was $0.2 million, consisting entirely of purchases of property and equipment.

Current wording

During the nine months ended September 30, 2025, net cash used in investing activities was $0.2 million, consisting entirely of purchases of property and equipment.

Previous wording

During the six months ended June 30, 2024, net cash provided by investing activities was $1.2 million, consisting of a $1.4 million sale of a restricted investment relating to a security deposit on one of our leases that was reclassified as restricted cash, partially offset by $0.2 million of purchases of property and equipment.

Current wording

During the nine months ended September 30, 2024, net cash provided by investing activities was $142.4 million, consisting of $141.3 million of proceeds from the sale of the VOWST Business and a $1.4 million sale of a restricted investment relating to a security deposit on one of our leases that was reclassified as restricted cash, partially offset by $0.3 million of purchases of property and equipment.

Previous wording

During the six months ended June 30, 2025, net cash provided by financing activities was $1.2 million, consisting of $1.0 million from the issuance of common stock under our at the market equity program, net of issuance costs and $0.2 million from the issuance of common stock under our 2015 Employee Stock Purchase Plan, or ESPP.

Current wording

During the nine months ended September 30, 2025, net cash provided by financing activities was $1.2 million, consisting of $1.0 million from the issuance of common stock under our at the market equity program, net of issuance costs and $0.2 million from the issuance of common stock under our 2015 Employee Stock Purchase Plan, or ESPP.

Previous wording

During the six months ended June 30, 2024, net cash provided by financing activities was $18.8 million, consisting of $18.4 million from the issuance of common stock under our at the market equity program, net of issuance costs and $0.4 million in connection with the issuance of common stock under our ESPP.

Current wording

During the nine months ended September 30, 2024, net cash used in financing activities was $92.1 million, consisting of $127.9 million repayment of the Oaktree Term Loan, partially offset by $21.8 million from the issuance of common stock under our at the market equity program, net of issuance costs, $13.5 million from the issuance of common stock in connection with the sale of the VOWST Business to SPN, and $0.5 million from the issuance of common stock under our 2015 ESPP.

Previous wording

the costs, timing and revenue, if any, of future commercialization activities, including manufacturing, marketing, sales and distribution, for any of our product candidates for which we receive marketing approval;

Current wording

the costs, timing and revenue, if any, of potential future commercialization activities, including manufacturing, marketing, sales and distribution, for any of our product candidates for which we receive marketing approval;

Previous wording

As discussed in Note 1 of the condensed consolidated financial statements included elsewhere in this Quarterly Report on Form 10-Q, we have the responsibility to evaluate whether conditions or events raise substantial doubt about our ability to meet our future financial obligations as they become due within 12 months after the date the condensed consolidated financial statements are issued. The ability to obtain sufficient proceeds from additional equity offerings, collaborations or other financing with terms favorable or acceptable to us cannot be considered probable, as these events are outside of our control. Accordingly, management has concluded that these circumstances raise substantial doubt about our ability to continue as a going concern. Based on our currently available cash resources, including the capital obtained from the Transaction, and considering our future operating plans and our ongoing obligations related to the Transaction, we anticipate that we will require additional funding in the first quarter of 2026.

Current wording

As discussed in Note 1 of the condensed consolidated financial statements included elsewhere in this Quarterly Report on Form 10-Q, we have the responsibility to evaluate whether conditions or events raise substantial doubt about our ability to meet our future financial obligations as they become due within 12 months after the date the condensed consolidated financial statements are issued. The ability to obtain sufficient proceeds from additional equity offerings, collaborations or other financing with terms favorable or acceptable to us cannot be considered probable, as these events are outside of our control. Accordingly, management has concluded that these circumstances raise substantial doubt about our ability to continue as a going concern. Based on our currently available cash resources, including proceeds received in the fourth quarter from our at the market equity offering, and considering our future operating plans and our ongoing obligations related to the Transaction, we anticipate that we will fund our operations through the second quarter of 2026.